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The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR.

Shen XX, Liang D, Zhang P - PLoS ONE (2012)

Bottom Line: For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups.We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species.In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.

ABSTRACT

Background: Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics.

Methodology/principal findings: We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR.

Conclusions/significance: Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for phylogenetic questions of osteichthyans at different taxonomic levels.

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Related in: MedlinePlus

Phylogram derived from analysis of the concatenated four long NPCL markers.Phylogenetic relationships among osteichthyans were based on maximum likelihood and Bayesian inference analyses of the combined data set (7,134 bp) under 3-partition and 4-partition strategies (by codon and by gene). The two quarter circles above the branches represent the bootstrap proportions for partitioned ML analyses and the two quarter circles below branches represent the Bayesian posterior probabilities for partitioned BI analyses. Branch lengths were estimated in the 4-partition ML (by gene) analysis on a concatenated dataset (4 GTR +Γ+I models for 4 gene partitions).
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pone-0039256-g003: Phylogram derived from analysis of the concatenated four long NPCL markers.Phylogenetic relationships among osteichthyans were based on maximum likelihood and Bayesian inference analyses of the combined data set (7,134 bp) under 3-partition and 4-partition strategies (by codon and by gene). The two quarter circles above the branches represent the bootstrap proportions for partitioned ML analyses and the two quarter circles below branches represent the Bayesian posterior probabilities for partitioned BI analyses. Branch lengths were estimated in the 4-partition ML (by gene) analysis on a concatenated dataset (4 GTR +Γ+I models for 4 gene partitions).

Mentions: The refined alignments of RAG1, KIAA1239, SACS, TTN are 1,488 nt, 1,737 nt, 2,211 nt, 1,698 nt in length, respectively. The BI and ML analyses on the concatenated dataset (7,134 nt) under the three different partitioning strategies (3-partition, 4 partition, and 12-partition) produce the same topology and similar support values. Most nodes (85%) are strongly supported with ≥95 bootstrap values (BS) and 1.0 Bayesian posterior probabilities (PP) (Fig. 3). The well-resolved tree inferred from the concatenated dataset (Fig. 3) generally agrees with the currently accepted osteichthyan phylogeny.


The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR.

Shen XX, Liang D, Zhang P - PLoS ONE (2012)

Phylogram derived from analysis of the concatenated four long NPCL markers.Phylogenetic relationships among osteichthyans were based on maximum likelihood and Bayesian inference analyses of the combined data set (7,134 bp) under 3-partition and 4-partition strategies (by codon and by gene). The two quarter circles above the branches represent the bootstrap proportions for partitioned ML analyses and the two quarter circles below branches represent the Bayesian posterior probabilities for partitioned BI analyses. Branch lengths were estimated in the 4-partition ML (by gene) analysis on a concatenated dataset (4 GTR +Γ+I models for 4 gene partitions).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375249&req=5

pone-0039256-g003: Phylogram derived from analysis of the concatenated four long NPCL markers.Phylogenetic relationships among osteichthyans were based on maximum likelihood and Bayesian inference analyses of the combined data set (7,134 bp) under 3-partition and 4-partition strategies (by codon and by gene). The two quarter circles above the branches represent the bootstrap proportions for partitioned ML analyses and the two quarter circles below branches represent the Bayesian posterior probabilities for partitioned BI analyses. Branch lengths were estimated in the 4-partition ML (by gene) analysis on a concatenated dataset (4 GTR +Γ+I models for 4 gene partitions).
Mentions: The refined alignments of RAG1, KIAA1239, SACS, TTN are 1,488 nt, 1,737 nt, 2,211 nt, 1,698 nt in length, respectively. The BI and ML analyses on the concatenated dataset (7,134 nt) under the three different partitioning strategies (3-partition, 4 partition, and 12-partition) produce the same topology and similar support values. Most nodes (85%) are strongly supported with ≥95 bootstrap values (BS) and 1.0 Bayesian posterior probabilities (PP) (Fig. 3). The well-resolved tree inferred from the concatenated dataset (Fig. 3) generally agrees with the currently accepted osteichthyan phylogeny.

Bottom Line: For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups.We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species.In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.

ABSTRACT

Background: Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics.

Methodology/principal findings: We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR.

Conclusions/significance: Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for phylogenetic questions of osteichthyans at different taxonomic levels.

Show MeSH
Related in: MedlinePlus